The Big Four firm, which audits the FAI, alerted the Companies Registration Office that "proper books of accounts are not kept" at the national football governing body. Deloitte also said the FAI had breached the Companies Act, according to reports.
The FAI has found itself at the centre of a financial storm in recent weeks, after it was revealed that its long-standing chief executive John Delaney had loaned the association €100,000 in 2017.
Delaney and the rest of the board will now resign within the next two months, before its annual general meeting in July.
Last week it was announced that accountancy firm Grant Thornton had been brought in by the FAI to examine "books, records and ledgers". In addition, Mazars was in the process of an "independent and in-depth external review of matters".